Identification and characterization of Colletotrichum species causing grape ripe rot in southern China

Isolates of Colletotrichum truncatum with Resistance to Multiple Fungicides from Soybean in Northern Thailand

In Thailand, four systemic fungicides-carbendazim (Car), azoxystrobin (Azo), difenoconazole (Dif), and penthiopyrad (Pen)-are commonly used to control soybean anthracnose caused by Colletotrichum truncatum; however, the pathogen has developed resistance. From 2019 to 2020, fungicide resistance in C. truncatum from fields in Chiang Rai and Chiang Mai was monitored. In tests of 85 C. truncatum isolates for resistance to multiple fungicides, 15.3% were CarRAzoR, 34.1% were triple resistant (CarRAzoRDifR or CarRAzoRPenR), and 50.6% were CarRAzoRDifRPenR. Surprisingly, all isolates tested had lost their sensitivity to one or more of the fungicides tested. The carbendazim-resistant isolates carried a point mutation in the β-tubulin gene at codon 198 (E198A) or 200 (F200Y), and all azoxystrobin-resistant isolates had a mutation in the cytochrome b gene at codon 143 (G143A) or 129 (F129L). Moreover, a novel mutation at codon 208 (S208Y) in the gene encoding succinate dehydrogenase subunit B was detected in all of the isolates highly resistant to penthiopyrad. No mutation linked with difenoconazole resistance was detected in the genes encoding cytochrome P450 sterol 14α-demethylase. To the best of our knowledge, this is the first report of C. truncatum isolates resistant to multiple fungicides and serves as a warning to take measures to prevent the occurrence and distribution of these multiple-fungicide-resistant populations in soybean fields.

Insights into Grape Ripe Rot: A Focus on the Colletotrichum gloeosporioides Species Complex and Its Management Strategies

Grape ripe rot, which is predominantly caused by the Colletotrichum species, presents a growing threat to global grape cultivation. This threat is amplified by the increasing populations of the Colletotrichum species in response to warmer climates. In this review, we investigate the wide-ranging spectrum of grape ripe rot, specifically highlighting the role and characteristics of the C. gloeosporioides species complex (CGSC). We incorporate this understanding as we explore the diverse symptoms that lead to infected grapevines, their intricate life cycle and epidemiology, and the escalating prevalence of C. viniferum in Asia and globally. Furthermore, we delve into numerous disease management strategies, both conventional and emerging, such as prevention and mitigation measures. These strategies include the examination of host resistances, beneficial cultivation practices, sanitation measures, microbiome health maintenance, fungicide choice and resistance, as well as integrated management approaches. This review seeks to enhance our understanding of this globally significant disease, aspiring to assist in the development and improvement of effective prevention and control strategies.

Ontogenic Susceptibility of Grapevine Clusters to Ripe Rot, Caused by the Colletotrichum acutatum and C. gloeosporioides Species Complexes

Natural infection by Colletotrichum spp. and the subsequent development of ripe rot were observed in susceptible grape (Vitis vinifera) clusters either protected or exposed to environmental conditions and naturally occurring inoculum by the application or removal of paper bags at various phenological stages at two Mid-Atlantic vineyards. During each of the three experimental seasons, most treatments with grape clusters that were exposed between veraison and harvest developed significantly more severe ripe rot than clusters that were exposed during only the early season or protected throughout the entire season. Spore traps were placed in one vineyard over two seasons and were analyzed via quantitative PCR. DNA of the Colletotrichum acutatum and C. gloeosporioides species complexes was detected from the bloom to the harvest stage, with a higher quantity of C. acutatum DNA than C. gloeosporioides DNA. From ripe rot symptomatic clusters, 417 isolates were collected, and a multilocus phylogenetic analysis of 51 representative isolates identified six Colletotrichum spp., with C. fioriniae (C. acutatum complex) being the most frequently isolated. Weather data were also monitored, and ripe rot-conducive conditions were observed at multiple times throughout each season. In summary, only clusters that were exposed to inoculum and environmental conditions in the late season developed severe ripe rot. The data collected in this study suggest that grape clusters have ontogenic susceptibility to ripe rot, becoming more susceptible as they mature, in contrast to the susceptible bloom stage for other fruit rotting diseases of grapevine.

Genome Sequence Resource for Colletotrichum viniferum, the Cause of Grapevine Ripe Rot in China

Grape ripe rot is an important disease that has seriously damaged the yield and quality of grape worldwide. The disease is caused by Colletotrichum viniferum, a hemibiotrophic fungus that belongs to the Glomerellaceae family of Sordariomycetes class. Here, we present the genome of C. viniferum CvYL2a from grape, based on Illumina HiSeq 2500 and PacBio RS II. The high-quality genome consists of 70 contigs with a 73.41 Mb genome size and encodes 14,668 protein-coding genes. These genes were annotated using Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, EuKaryotic Orthologous Groups, Nonredundant Protein, and Swiss-Prot databases. In addition, we identified a series of genes involved in pathogenicity, including 909 carbohydrate-active enzymes, 67 secondary metabolite gene clusters, and 307 cytochrome P450 enzymes. This genome sequence provides a valuable reference for research on grape-C. viniferum interactions, the pathogenesis of C. viniferum, and comparative genome analyses.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Pest categorisation of Colletotrichum plurivorum

The EFSA Plant Health Panel performed a pest categorisation of Colletotrichum plurivorum Damm, Alizadeh & Toy. Sato, a well-defined fungus of the C. orchidearum species complex which has been reported from Africa, Asia and America to cause anthracnose and pre- and post-harvest fruit rots on more than 30 plant genera. The pathogen has not been reported from the EU territory and is not included in EU Commission Implementing Regulation 2019/2072. Because of the very wide host range, this pest categorisation focused on Abelmoschus esculentus, Capsicum spp., Carica papaya, Glycine max, Manihot esculenta, Phaseolus lunatus, Pyrus bretschneideri and Vitis spp. for which there was robust evidence that C. plurivorum was formally identified by morphology and multilocus gene sequencing analysis. Host plants for planting and fresh fruits are the main pathways for the entry of the pathogen into the EU. The host availability and climate suitability factors occurring in some parts of the EU are favourable for the establishment of the pathogen. Economic impact on the production of the main hosts is expected if establishment occurs. Phytosanitary measures are available to prevent the introduction of the pathogen into the EU. Colletotrichum plurivorum satisfies the criteria that are within the remit of EFSA to assess for this species to be regarded as a potential Union quarantine pest. However, there is a high uncertainty on the status of C. plurivorum in the EU territory because of the lack of specific surveys following the re-evaluation of the taxonomy of the genus Colletotrichum.

Managing Colletotrichum on Fruit Crops: A "Complex" Challenge

The fungal genus Colletotrichum includes numerous important plant pathogenic species and species complexes that infect a wide variety of hosts. Its taxonomy is particularly complex because species' phenotypes and genotypes are difficult to differentiate. Two notable complexes, C. acutatum and C. gloeosporioides, are known for infecting temperate fruit crops worldwide. Even species within these complexes vary in traits such as tissue specificity, aggressiveness, geographic distribution, and fungicide sensitivity. With few effective chemicals available to control these pathogens, and the persistent threat of fungicide resistance, there is a need for greater understanding of this destructive genus and the methods that can be used for disease management. This review summarizes current research on diseases caused by Colletotrichum spp. on major fruit crops in the United States, focusing on the taxonomy of species involved, disease management strategies, and future management outlook.

The Colletotrichum dracaenophilum, C. magnum and C. orchidearum species complexes

Although Glomerella glycines, Colletotrichum magnum and C. orchidearum are known as causal agents of anthracnose of soybean, Cucurbitaceae and Orchidaceae, respectively, their taxonomy remains unresolved. In preliminary analyses based on ITS, strains of these species appear basal in Colletotrichum phylogenies, clustering close to C. cliviae, C. brevisporum and other recently described species from tropical or subtropical regions. Phylogenetic analyses (ITS, GAPDH, CHS-1, HIS3, ACT, TUB2) of 102 strains previously identified as Ga. glycines, C. magnum and C. orchidearum as well as other related strains from different culture collections and studies placed these taxa in three species complexes, and distinguished at least 24 species, including 11 new species. In this study, C. magnum, C. orchidearum and C. piperis were epitypified and their taxonomy resolved, while C. cliviicola was proposed as a new name for C. cliviae. Furthermore, a sexual morph was observed for C. yunnanense, while C. brevisporum, C. cliviicola and C. tropicicola were reported from new hosts or countries. Regarding their conidial morphology, species in the C. dracaenophilum, C. magnum and C. orchidearum species complexes are reminiscent of C. gloeosporioides or C. boninense s. lat., and were likely to be confused with them in the past.

Colletotrichum species associated to ripe rot disease of grapes in the “Serra Gaucha” region of Southern Brazil

Ripe rot disease caused by Colletotrichum (Glomerella) has become a serious problem for viticulture in Southern Brazil. Global warming contributes to the increase of this devastating and difficult to control disease. Several species of Colletotrichum, with different phytopathological characteristics, have been associated with ripe rot disease in different viticultural regions. In this article, a total of 63 fungi were isolated from grapes showing symptoms of ripe rot disease, and classified by sequencing of ITS region, and compared with the sequences deposited in GenBank. The isolates were included in three clades of Colletotrichum: 84.1% belonged to the “gloeosporioides” clade, 3.2% to the “boninense” clade, and 12.7% to the “acutatum” clade. Of the 53 isolates included in the “gloeosporioides” clade, 44.4% were classified as C. viniferum/C. ampelinum, 37.1% as C. fruticola, 13.0% as C. kahawae and 5.5% as a species related to C. fruticola. In turn, the two isolates of the “boninense” clade were classified as C. kartii/C. phyllanthi, and the six “acutatum” isolates were similar to C. acutatum and C. nymphaeae reference materials. The identified species were previously linked to ripe rot disease in other viticulture regions of the world, but the frequency of some species in southern Brazil is particularly different.

Epidemiology, pathology and identification of Colletotrichum including a novel species associated with avocado (Persea americana) anthracnose in Israel

Anthracnose disease caused by Colletotrichum species is a major constraint for the shelf-life and marketability of avocado fruits. To date, only C. gloeosporioides sensu lato and C. aenigma have been reported as pathogens affecting avocado in Israel. This study was conducted to identify and characterize Colletotrichum species associated with avocado anthracnose and to determine their survival on different host-structures in Israel. The pathogen survived and over-wintered mainly on fresh and dry leaves, as well as fresh twigs in the orchard. A collection of 538 Colletotrichum isolates used in this study was initially characterized based on morphology and banding patterns generated according to arbitrarily primed PCR to assess the genetic diversity of the fungal populations. Thereafter, based on multi-locus phylogenetic analyses involving combinations of ITS, act, ApMat, cal, chs1, gapdh, gs, his3, tub2 gene/markers; eight previously described species (C. aenigma, C. alienum, C. fructicola, C. gloeosporioides sensu stricto, C. karstii, C. nupharicola, C. siamense, C. theobromicola) and a novel species (C. perseae) were identified, as avocado anthracnose pathogens in Israel; and reconfirmed after pathogenicity assays. Colletotrichum perseae sp. nov. and teleomorph of C. aenigma are described along with comprehensive morphological descriptions and illustrations, for the first time in this study.